As above;)
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I used a key with a flat battery for a couple of weeks with no immobiliser issues. The only embarassing thing was getting in through the passenger door manually and having to get the key into the ignition quickly to stop the alarm.
If you still have the D3 then in theory, it doesn't go flat as it's recharging whenever it's in the ignition. ;)
If (for some reason) it's flat, then as indicated above, you can use the manual key to unlock the front passenger door (after prying off the plastic handle cover) and get in and insert the key. You'd expect enough voltage to dis-arm the immobilizer once you turn the ignition on.
Cheers,
Gordon
The last post has it... D3 key batteries are different to D4 ones. Ean has a D3, so listen to Gordon.